Personally I would keep him in the QT. Under the skin fish are just <coff> fish food and you don't want other fish nibbling at him. To further reduce the risk of infection I would up the daily water changes to 75% (again much easier if he is in the QT) and use aquarium salt at a dosage of 1 tablespoon per 10 litres. Dissolve this in water before adding to the tank. When you do a water change only add enough salt for the water you are replacing. Keep him in the salt for 2 weeks and then stop adding salt when you do the water changes.
Thanks for your reply. Since adding him into the main tank his colours are back to normal and seems so much happier. I'll keep a close eye on him for the next few days, if I see no progress I'll put him into quarantine tank again and will do what you suggest, thanks.